Brownian dynamics simulations of fluorescence fluctuation spectroscopy

Area of Science:

• Biophysics
• Computational Chemistry
• Spectroscopy

Background:

• Fluorescence fluctuation analysis is crucial for studying biomolecular dynamics.
• Simulating these fluctuations, especially in diluted samples, presents computational challenges.
• Existing models may not fully capture hydrodynamic interactions or scanning effects.

Purpose of the Study:

• To develop a computational program for simulating fluorescence fluctuations in diluted (bio)molecular samples.
• To validate the simulation accuracy for translational diffusion and hydrodynamic interactions.
• To apply the model to scanning fluorescence correlation spectroscopy (FCS) and photon counting histograms.

Main Methods:

• Developed a simulation program incorporating periodic boundary conditions for constant concentration (0.5-10 nM).
• Simulated fluorescence correlation functions on limited system sizes, requiring 100-300 times the diffusion relaxation time.
• Applied the model to simulate scanning FCS and photon counting histograms for confocal microscopy.

Main Results:

• Accurate computation of fluorescence correlation functions is achievable on small systems.
• Simulations of scanning FCS at ~0.5 nM showed anticorrelation effects, less pronounced at higher concentrations.
• Anticorrelation effects in scanning FCS are potentially linked to non-uniform fluorophore distribution.

Conclusions:

• The developed simulation program accurately models fluorescence fluctuations and diffusion dynamics.
• The model is effective for analyzing highly diluted samples using techniques like scanning FCS.
• Observed anticorrelation effects in scanning FCS provide insights into fluorophore distribution dynamics.